WASHINGTON—When federal regulators launched a crackdown on alleged discrimination in auto lending two years ago, they knew their methodology would be questioned. But they calculated they could secure a market-shaping settlement by going after a company unlikely to fight the charges because it needed to avoid a complaint to clinch government approval for a broader restructuring.

That is the conclusion of a report, based on internal documents and emails written by the staff of the Consumer Financial Protection Bureau, released Tuesday by...